<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:10pt"><div><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">Dear Gromacs Users,</font></div><div><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2"><br></font></div><div><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2"><span class="Apple-style-span" style="white-space: pre; ">I am using the -rerun option of mdrun to re-analyze a trajectory. Thus, I tried to rerun the same </span></font><span class="Apple-style-span" style="font-family: verdana, helvetica, sans-serif; white-space: pre; font-size: 13px; ">trajectory (md.xtc) with exactly the same md.tpr. </span></div><div><span class="Apple-style-span" style="font-family: verdana, helvetica, sans-serif; white-space: pre; font-size: 13px; ">But the bonded interactions are not computed or written to the log
file or to the .edr file, resulting to completely different energy values from the initial log and edr files.</span></div><div><pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">I am using the following command, in order to read the coordinates stored in the .xtc file and compute the potential energy:</font></pre><pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">mdrun -rerun md.xtc -s md.tpr <br></font></pre><pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2"><br></font></pre><pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">Thanks in advance for your help</font></pre></div></div></body></html>